[Strategy Market] Loops & Stacks

Loops/unpaired bases (excluding locked bases):
1 point for every unpaired A
0.5 points for every unpaired G

2 points for every GC pair at the end of a stack
1 point for every GC pair not at the end of a stack
1 point for every AU pair at the end of a stack
2 points for every AU pair not at the end of a stack
1 point for every GU pair

Modifier = 1 - abs((number of GC pairs)/(total number of pairs) - 0.55)

Score = 100 * (modifier) * (total number of points)/(total number of bases excluding locked unpaired bases)

Dear aldo,

Your strategy has been added to our implementation queue with task id 6. You can check the schedule of the implementation here.

ETA of the implementation is tomorrow 6/4/2011

Thanks for sharing your idea!

EteRNA team

Dear aldo,

We are glad to report that your strategy has been implemented and tested.

While implementing your strategy, we have made small changes to the parameters you specified to optimize the performance. Specifically, parameters 2,1,1,2,1 (points) had minor changes.

Note that we’ll always run a optimization over the parameters you specify, so you won’t have to worry about fine tuning all the numbers you use. Just the idea and rough numbers are enough to run your algorithm!

Length : Your strategy was implmented with 40 line of code.

Ordering : We ran your strategy on all synthesized designs and ordered them based on predicted scores. The correlation of your strategy’s ordering with the ordering based on the actual scores was 0.407. (1.0 is the best score, -1.0 is the worst score. A completely random prediction would have 0 correlation)

Please note that the numbers specified above will change in future as we’ll rerun your algorithm whenever new synthesis data is available.

More detailed result has been posted on the strategy market page. Thank you for sharing your idea, and we look forward to other brilliant strategies from you!

Dear aldo,

We made a change in the way we score the ordering. (Detail : Before if your algorithm said score of A and B is the same when they are not, it decreased your ordering score. In the new scoring, such decision does neither increase nor decreases your ordering score).

Your ordering score is now 0.454